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For: Grigoriev A. A relationship between gene expression and protein interactions on the proteome scale: analysis of the bacteriophage T7 and the yeast Saccharomyces cerevisiae. Nucleic Acids Res 2001;29:3513-9. [PMID: 11522820 PMCID: PMC55876 DOI: 10.1093/nar/29.17.3513] [Citation(s) in RCA: 179] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]  Open
Number Cited by Other Article(s)
1
Adhikari P, Jawad B, Ching WY. Electronic Interactions Between the Receptor-Binding Domain of Omicron Variants and Angiotensin-Converting Enzyme 2: A Novel Amino Acid-Amino Acid Bond Pair Concept. Molecules 2025;30:2061. [PMID: 40363865 PMCID: PMC12073306 DOI: 10.3390/molecules30092061] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2025] [Revised: 04/29/2025] [Accepted: 05/01/2025] [Indexed: 05/15/2025]  Open
2
Tilajka Á, Kurilla A, László L, Lovrics A, Novák J, Takács T, Buday L, Vas V. Predictive value analysis of the interaction network of Tks4 scaffold protein in colon cancer. Front Mol Biosci 2024;11:1414805. [PMID: 39234565 PMCID: PMC11371697 DOI: 10.3389/fmolb.2024.1414805] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2024] [Accepted: 07/31/2024] [Indexed: 09/06/2024]  Open
3
Tang T, Zhang X, Li W, Wang Q, Liu Y, Cao X. Co-training based prediction of multi-label protein-protein interactions. Comput Biol Med 2024;177:108623. [PMID: 38788374 DOI: 10.1016/j.compbiomed.2024.108623] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2024] [Revised: 05/01/2024] [Accepted: 05/16/2024] [Indexed: 05/26/2024]
4
Nithya C, Kiran M, Nagarajaram HA. Hubs and Bottlenecks in Protein-Protein Interaction Networks. Methods Mol Biol 2024;2719:227-248. [PMID: 37803121 DOI: 10.1007/978-1-0716-3461-5_13] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/08/2023]
5
Wu S, Wagner G. Protocol to analyze dysregulation of the eIF4F complex in human cancers using R software and large public datasets. STAR Protoc 2022;3:101880. [PMID: 36595939 PMCID: PMC9768376 DOI: 10.1016/j.xpro.2022.101880] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2022] [Revised: 09/08/2022] [Accepted: 11/02/2022] [Indexed: 12/14/2022]  Open
6
Li Z, Wang W, Ma B, Yin J, Hu C, Luo P, Wang Y. Genomic and biological characteristics of a newly isolated lytic bacteriophage PZJ0206 infecting the Enterobacter cloacae. Virus Res 2022;316:198800. [DOI: 10.1016/j.virusres.2022.198800] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2021] [Revised: 04/26/2022] [Accepted: 05/06/2022] [Indexed: 10/18/2022]
7
Evans-Yamamoto D, Rouleau FD, Nanda P, Makanae K, Liu Y, Després P, Matsuo H, Seki M, Dubé AK, Ascencio D, Yachie N, Landry C. OUP accepted manuscript. Nucleic Acids Res 2022;50:e54. [PMID: 35137167 PMCID: PMC9122585 DOI: 10.1093/nar/gkac045] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2021] [Revised: 12/22/2021] [Accepted: 01/14/2022] [Indexed: 11/13/2022]  Open
8
Farooq QUA, Shaukat Z, Aiman S, Li CH. Protein-protein interactions: Methods, databases, and applications in virus-host study. World J Virol 2021;10:288-300. [PMID: 34909403 PMCID: PMC8641042 DOI: 10.5501/wjv.v10.i6.288] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/15/2021] [Revised: 04/19/2021] [Accepted: 07/30/2021] [Indexed: 02/06/2023]  Open
9
Grigoriev A. Transfer RNA and Origins of RNA Interference. Front Mol Biosci 2021;8:708984. [PMID: 34368233 PMCID: PMC8343393 DOI: 10.3389/fmolb.2021.708984] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2021] [Accepted: 07/08/2021] [Indexed: 01/21/2023]  Open
10
Spatiotemporal 22q11.21 Protein Network Implicates DGCR8-Dependent MicroRNA Biogenesis as a Risk for Late-Fetal Cortical Development in Psychiatric Diseases. Life (Basel) 2021;11:life11060514. [PMID: 34073122 PMCID: PMC8227527 DOI: 10.3390/life11060514] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2021] [Revised: 05/28/2021] [Accepted: 05/31/2021] [Indexed: 12/28/2022]  Open
11
Fluorescence resonance energy transfer in revealing protein-protein interactions in living cells. Emerg Top Life Sci 2021;5:49-59. [PMID: 33856021 DOI: 10.1042/etls20200337] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2020] [Revised: 02/22/2021] [Accepted: 03/04/2021] [Indexed: 11/17/2022]
12
Kandel A, Dhillon SK, Prabaharan CB, Fatnin Binti Hisham S, Rajamanickam K, Napper S, Chidambaram SB, Essa MM, Yang J, Sakharkar MK. Identifying kinase targets of PPARγ in human breast cancer. J Drug Target 2021;29:660-668. [PMID: 33496213 DOI: 10.1080/1061186x.2021.1877719] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
13
Chen Q, Li Y, Tan K, Qiao Y, Pan S, Jiang T, Chen YPP. Network-based methods for gene function prediction. Brief Funct Genomics 2021;20:249-257. [PMID: 33686431 DOI: 10.1093/bfgp/elab006] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2020] [Revised: 01/25/2021] [Accepted: 01/26/2021] [Indexed: 12/23/2022]  Open
14
Cope AL, O'Meara BC, Gilchrist MA. Gene expression of functionally-related genes coevolves across fungal species: detecting coevolution of gene expression using phylogenetic comparative methods. BMC Genomics 2020;21:370. [PMID: 32434474 PMCID: PMC7240986 DOI: 10.1186/s12864-020-6761-3] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2020] [Accepted: 04/29/2020] [Indexed: 11/23/2022]  Open
15
Nathan KG, Lal SK. The Multifarious Role of 14-3-3 Family of Proteins in Viral Replication. Viruses 2020;12:E436. [PMID: 32294919 PMCID: PMC7232403 DOI: 10.3390/v12040436] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2020] [Revised: 04/06/2020] [Accepted: 04/07/2020] [Indexed: 02/06/2023]  Open
16
Li X, Li W, Zeng M, Zheng R, Li M. Network-based methods for predicting essential genes or proteins: a survey. Brief Bioinform 2020;21:566-583. [PMID: 30776072 DOI: 10.1093/bib/bbz017] [Citation(s) in RCA: 67] [Impact Index Per Article: 13.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2018] [Revised: 01/21/2019] [Accepted: 01/22/2019] [Indexed: 01/03/2025]  Open
17
Sabir JSM, El Omri A, Banaganapalli B, Aljuaid N, Omar AMS, Altaf A, Hajrah NH, Zrelli H, Arfaoui L, Elango R, Alharbi MG, Alhebshi AM, Jansen RK, Shaik NA, Khan M. Unraveling the role of salt-sensitivity genes in obesity with integrated network biology and co-expression analysis. PLoS One 2020;15:e0228400. [PMID: 32027667 PMCID: PMC7004317 DOI: 10.1371/journal.pone.0228400] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2019] [Accepted: 01/14/2020] [Indexed: 02/07/2023]  Open
18
Zhang J, Ju S. Identifying genuine protein-protein interactions within communities of gene co-expression networks using a deconvolution method. IET Syst Biol 2019;13:290-296. [PMID: 31778125 PMCID: PMC8687158 DOI: 10.1049/iet-syb.2019.0060] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2019] [Revised: 06/24/2019] [Accepted: 07/09/2019] [Indexed: 11/20/2022]  Open
19
Konda AK, Sabale PR, Soren KR, Subramaniam SP, Singh P, Rathod S, Chaturvedi SK, Singh NP. Systems Biology Approaches Reveal a Multi-stress Responsive WRKY Transcription Factor and Stress Associated Gene Co-expression Networks in Chickpea. Curr Bioinform 2019. [DOI: 10.2174/1574893614666190204152500] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
20
Guala D, Ogris C, Müller N, Sonnhammer ELL. Genome-wide functional association networks: background, data & state-of-the-art resources. Brief Bioinform 2019;21:1224-1237. [PMID: 31281921 PMCID: PMC7373183 DOI: 10.1093/bib/bbz064] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2019] [Revised: 04/29/2019] [Accepted: 05/04/2019] [Indexed: 02/06/2023]  Open
21
Zhao J, Lei Y, Hong J, Zheng C, Zhang L. AraPPINet: An Updated Interactome for the Analysis of Hormone Signaling Crosstalk in Arabidopsis thaliana. FRONTIERS IN PLANT SCIENCE 2019;10:870. [PMID: 31333706 PMCID: PMC6625390 DOI: 10.3389/fpls.2019.00870] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/08/2019] [Accepted: 06/18/2019] [Indexed: 05/29/2023]
22
Rasti S, Vogiatzis C. A survey of computational methods in protein–protein interaction networks. ANNALS OF OPERATIONS RESEARCH 2019;276:35-87. [DOI: 10.1007/s10479-018-2956-2] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/03/2025]
23
Sabir JSM, El Omri A, Shaik NA, Banaganapalli B, Al-Shaeri MA, Alkenani NA, Hajrah NH, Awan ZA, Zrelli H, Elango R, Khan M. Identification of key regulatory genes connected to NF-κB family of proteins in visceral adipose tissues using gene expression and weighted protein interaction network. PLoS One 2019;14:e0214337. [PMID: 31013288 PMCID: PMC6478283 DOI: 10.1371/journal.pone.0214337] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2019] [Accepted: 03/11/2019] [Indexed: 12/12/2022]  Open
24
Nam Y, Jhee JH, Cho J, Lee JH, Shin H. Disease gene identification based on generic and disease-specific genome networks. Bioinformatics 2018;35:1923-1930. [DOI: 10.1093/bioinformatics/bty882] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2018] [Revised: 10/11/2018] [Accepted: 10/17/2018] [Indexed: 01/11/2023]  Open
25
Zhang L, Liu JY, Gu H, Du Y, Zuo JF, Zhang Z, Zhang M, Li P, Dunwell JM, Cao Y, Zhang Z, Zhang YM. Bradyrhizobium diazoefficiens USDA 110- Glycine max Interactome Provides Candidate Proteins Associated with Symbiosis. J Proteome Res 2018;17:3061-3074. [PMID: 30091610 DOI: 10.1021/acs.jproteome.8b00209] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
26
Ding Z, Kihara D. Computational Methods for Predicting Protein-Protein Interactions Using Various Protein Features. CURRENT PROTOCOLS IN PROTEIN SCIENCE 2018;93:e62. [PMID: 29927082 PMCID: PMC6097941 DOI: 10.1002/cpps.62] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
27
Novel insights into global translational regulation through Pumilio family RNA-binding protein Puf3p revealed by ribosomal profiling. Curr Genet 2018;65:201-212. [PMID: 29951697 DOI: 10.1007/s00294-018-0862-4] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2018] [Revised: 06/16/2018] [Accepted: 06/19/2018] [Indexed: 01/13/2023]
28
Mounika Inavolu S, Renbarger J, Radovich M, Vasudevaraja V, Kinnebrew GH, Zhang S, Cheng L. IODNE: An integrated optimization method for identifying the deregulated subnetwork for precision medicine in cancer. CPT-PHARMACOMETRICS & SYSTEMS PHARMACOLOGY 2017;6:168-176. [PMID: 28266149 PMCID: PMC5351413 DOI: 10.1002/psp4.12167] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/05/2016] [Revised: 01/05/2017] [Accepted: 01/06/2017] [Indexed: 12/18/2022]
29
Zhang K, Li Y, Li T, Li ZG, Hsiang T, Zhang Z, Sun W. Pathogenicity Genes in Ustilaginoidea virens Revealed by a Predicted Protein-Protein Interaction Network. J Proteome Res 2017;16:1193-1206. [PMID: 28099032 DOI: 10.1021/acs.jproteome.6b00720] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
30
Computational Approaches for Predicting Binding Partners, Interface Residues, and Binding Affinity of Protein-Protein Complexes. Methods Mol Biol 2017;1484:237-253. [PMID: 27787830 DOI: 10.1007/978-1-4939-6406-2_16] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
31
Jain S, Bader GD. Predicting physiologically relevant SH3 domain mediated protein-protein interactions in yeast. Bioinformatics 2016;32:1865-72. [PMID: 26861823 PMCID: PMC4908317 DOI: 10.1093/bioinformatics/btw045] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2015] [Revised: 12/05/2015] [Accepted: 01/20/2016] [Indexed: 12/02/2022]  Open
32
Zhang F, Liu S, Li L, Zuo K, Zhao L, Zhang L. Genome-Wide Inference of Protein-Protein Interaction Networks Identifies Crosstalk in Abscisic Acid Signaling. PLANT PHYSIOLOGY 2016;171:1511-22. [PMID: 27208273 PMCID: PMC4902594 DOI: 10.1104/pp.16.00057] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/13/2016] [Accepted: 04/14/2016] [Indexed: 05/24/2023]
33
Abundance and Temperature Dependency of Protein-Protein Interaction Revealed by Interface Structure Analysis and Stability Evolution. Sci Rep 2016;6:26737. [PMID: 27220911 PMCID: PMC4879665 DOI: 10.1038/srep26737] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2016] [Accepted: 05/06/2016] [Indexed: 11/08/2022]  Open
34
Bhardwaj J, Gangwar I, Panzade G, Shankar R, Yadav SK. Global De Novo Protein-Protein Interactome Elucidates Interactions of Drought-Responsive Proteins in Horse Gram (Macrotyloma uniflorum). J Proteome Res 2016;15:1794-809. [PMID: 27161830 DOI: 10.1021/acs.jproteome.5b01114] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
35
ProSim: A Method for Prioritizing Disease Genes Based on Protein Proximity and Disease Similarity. BIOMED RESEARCH INTERNATIONAL 2015;2015:213750. [PMID: 26339594 PMCID: PMC4538409 DOI: 10.1155/2015/213750] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/15/2014] [Accepted: 01/16/2015] [Indexed: 01/19/2023]
36
Lin GN, Corominas R, Lemmens I, Yang X, Tavernier J, Hill DE, Vidal M, Sebat J, Iakoucheva LM. Spatiotemporal 16p11.2 protein network implicates cortical late mid-fetal brain development and KCTD13-Cul3-RhoA pathway in psychiatric diseases. Neuron 2015;85:742-54. [PMID: 25695269 DOI: 10.1016/j.neuron.2015.01.010] [Citation(s) in RCA: 118] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2014] [Revised: 08/17/2014] [Accepted: 01/14/2015] [Indexed: 12/19/2022]
37
Anděl M, Kléma J, Krejčík Z. Network-constrained forest for regularized classification of omics data. Methods 2015;83:88-97. [PMID: 25872185 DOI: 10.1016/j.ymeth.2015.04.006] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2015] [Revised: 04/01/2015] [Accepted: 04/02/2015] [Indexed: 12/28/2022]  Open
38
Srihari S, Madhamshettiwar PB, Song S, Liu C, Simpson PT, Khanna KK, Ragan MA. Complex-based analysis of dysregulated cellular processes in cancer. BMC SYSTEMS BIOLOGY 2014;8 Suppl 4:S1. [PMID: 25521701 PMCID: PMC4290683 DOI: 10.1186/1752-0509-8-s4-s1] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
39
Networks' Characteristics Matter for Systems Biology. ACTA ACUST UNITED AC 2014;2:139-161. [PMID: 26500772 DOI: 10.1017/nws.2014.13] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
40
Kim Y, Jang JH, Choi S, Hwang D. TEMPI: probabilistic modeling time-evolving differential PPI networks with multiPle information. Bioinformatics 2014;30:i453-60. [PMID: 25161233 PMCID: PMC4147907 DOI: 10.1093/bioinformatics/btu454] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]  Open
41
Dhal PK, Barman RK, Saha S, Das S. Dynamic modularity of host protein interaction networks in Salmonella Typhi infection. PLoS One 2014;9:e104911. [PMID: 25144185 PMCID: PMC4140748 DOI: 10.1371/journal.pone.0104911] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2014] [Accepted: 07/17/2014] [Indexed: 01/08/2023]  Open
42
Lei D, Lin R, Yin C, Li P, Zheng A. Global protein-protein interaction network of rice sheath blight pathogen. J Proteome Res 2014;13:3277-93. [PMID: 24894516 DOI: 10.1021/pr500069r] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
43
Effective identification of essential proteins based on priori knowledge, network topology and gene expressions. Methods 2014;67:325-33. [DOI: 10.1016/j.ymeth.2014.02.016] [Citation(s) in RCA: 80] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2013] [Revised: 01/16/2014] [Accepted: 02/11/2014] [Indexed: 11/23/2022]  Open
44
Protein-protein interaction detection: methods and analysis. INTERNATIONAL JOURNAL OF PROTEOMICS 2014;2014:147648. [PMID: 24693427 PMCID: PMC3947875 DOI: 10.1155/2014/147648] [Citation(s) in RCA: 424] [Impact Index Per Article: 38.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 10/26/2013] [Revised: 12/05/2013] [Accepted: 12/20/2013] [Indexed: 12/24/2022]
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Grigoriev A. Understanding the yeast proteome: a bioinformatics perspective. Expert Rev Proteomics 2014;1:193-205. [PMID: 15966814 DOI: 10.1586/14789450.1.2.193] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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Srihari S, Raman V, Leong HW, Ragan MA. Evolution and Controllability of Cancer Networks: A Boolean Perspective. IEEE/ACM TRANSACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMATICS 2014;11:83-94. [PMID: 26355510 DOI: 10.1109/tcbb.2013.128] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
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Boucher B, Jenna S. Genetic interaction networks: better understand to better predict. Front Genet 2013;4:290. [PMID: 24381582 PMCID: PMC3865423 DOI: 10.3389/fgene.2013.00290] [Citation(s) in RCA: 55] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2013] [Accepted: 11/28/2013] [Indexed: 12/21/2022]  Open
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Lysis delay and burst shrinkage of coliphage T7 by deletion of terminator Tφ reversed by deletion of early genes. J Virol 2013;88:2107-15. [PMID: 24335287 DOI: 10.1128/jvi.03274-13] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]  Open
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Jüschke C, Dohnal I, Pichler P, Harzer H, Swart R, Ammerer G, Mechtler K, Knoblich JA. Transcriptome and proteome quantification of a tumor model provides novel insights into post-transcriptional gene regulation. Genome Biol 2013;14:r133. [PMID: 24289286 PMCID: PMC4053992 DOI: 10.1186/gb-2013-14-11-r133] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2013] [Accepted: 11/30/2013] [Indexed: 11/25/2022]  Open
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Schleker S, Ananthasubramanian S, Klein‐Seetharaman J, Ganapathiraju MK. Prediction of Intra‐ and Interspecies Protein–Protein Interactions Facilitating Systems Biology Studies. METHODS AND PRINCIPLES IN MEDICINAL CHEMISTRY 2013:21-53. [DOI: 10.1002/9783527648207.ch2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/03/2025]
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